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Improve circRNA-miRNA interaction analysis #166

Merged
merged 80 commits into from
Aug 8, 2024
Merged

Improve circRNA-miRNA interaction analysis #166

merged 80 commits into from
Aug 8, 2024

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mweyrich28
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Extending MIRNA_PREDICTION subworkflow:

  1. Adding MIRNA_NORMALIZATION (process): performs DESeq2 normalization.
    Adding MIRNA_FILTERING (process): filters output of MIRNA_NORMALISATION based on params.mirna_min_sample and params.mirna_min_percentage.
    Based on this, all samples that did not survive the filtering get removed from mature.
  2. Adding MIRNA_BINDINGSITES: This subworkflow performs binding site predictions with the specified tools in params.mirna_tools.
    The output of each tool gets converted into a unified format, which serves as an input for MAJORITY_VOTE.
    This process filters out binding sites, which were predicted by less than params.mirna_vote tools.
    MIRNA_BINDINGSITES can be extended with tools like TarpMIR (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018371/) and PITA (https://mybiosoftware.com/pita-6-microrna-prediction-tool.html) in the future.
  3. Adding COMPUTE_CORRELATIONS (process): computes correlations between miRNA and transcript expression levels,
    and writes the results to individual TSV files for each miRNA-target interaction specified in the input binding sites file.

This will be the entry point for the SPONGING analysis module mentioned in Issue 137.

LINT RESULTS SUMMARY
[✔] 569 Tests Passed
[?] 0 Tests Ignored
[!] 23 Test Warnings
[✗] 0 Tests Failed

mweyrich28 and others added 30 commits August 6, 2024 15:05
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@nictru nictru left a comment

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Making good progress

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@nictru
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nictru commented Aug 8, 2024

Do not forget this

@nictru nictru changed the title Sponging Improve circRNA-miRNA interaction analysis Aug 8, 2024
@nictru nictru added the enhancement Improvement for existing functionality label Aug 8, 2024
@nictru nictru added this to the Before release process milestone Aug 8, 2024
@mweyrich28 mweyrich28 merged commit b233bb8 into dev Aug 8, 2024
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